Molecular Docking
Tools and techniques for evaluating how strongly a ligand binds to a protein — the foundation of my drug-repurposing research.
Screening PTR1: A Real Target for Visceral Leishmaniasis
The library and the pipeline finally meet an actual disease target — pteridine reductase 1, from the parasite behind visceral leishmaniasis. First real screening result of the project.
Building an FDA-Approved Drug Library
Scaling up from docking one ligand at a time to screening almost two thousand real FDA-approved drugs in a single run — building the library, the ligand-prep pipeline, and a first pipeline smoke test.
Hello Tools 2
Continuing with step 2, demonstrate fPocket, basic work flow, and explination of a few of the stats generated by the tools.
Hello Tools 1
Step two is making sure the software works at the most basic level. Here we will us PyMol to view Human Serum Albumin and Wafarin before and after docking. We use Open Babel to convert the file format to a format AutoDockVina-GPU can use. Then we use AutoDockVina-GPU to perform the docking calculations.
Installing the software
fPocket - Used to detect cavities in a molecular structure
PyMOL - Used to visualize the structure of the molecules
AutoDock Vina - This is the software that actually calculates the docking strength.
Open Babel - Used to convert between different file formats